id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9826 Crash recording movie vsreddy@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-6.2.0-33-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x00007f32f37fe640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f32f3fff640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3310ff9640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/selectors.py"", line 416 in select File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f33117fa640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3311ffb640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f33127fc640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3312ffd640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f33137fe640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3313fff640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3330ff9640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f33317fa640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3331ffb640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f33327fc640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3332ffd640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f33337fe640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3333fff640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3378ff9640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f33797fa640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007f3379ffb640 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 910 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/usr/lib/ucsf-chimerax/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00007f33de69dc40 (most recent call first): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/OpenGL/GL/images.py"", line 369 in glReadPixels File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 1275 in frame_buffer_image File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 492 in image_rgba File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/movie/movie.py"", line 168 in capture_image File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 138 in invoke File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 237 in _activate File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 206 in activate File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 382 in activate_trigger File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 89 in draw_new_frame File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/std_commands/wait.py"", line 43 in draw_frame File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/std_commands/wait.py"", line 32 in wait File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py"", line 38 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py"", line 173 in _run_commands File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/scripting.py"", line 160 in open_command_script File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 435 in remember_data_format File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 447 in collated_open File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 194 in provider_open File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 119 in cmd_open File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py"", line 87 in _run_code File ""/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Thu Sep 21 21:26:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Thu Sep 21 18:27:05 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Sun Sep 17 10:41:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ad5wt_re3d_ctfref.mrc Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > open ad5wt_deltaIX_re3d_ctfref.mrc Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > ui tool show ""Map Coordinates"" > view orient > view initial > volume #1 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 style image region 0,0,396,799,799,396 step 1 showOutlineBox true > volume #1 style image region 0,0,396,799,799,396 step 1 showOutlineBox true > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > volume #1 region 0,0,0,799,799,799 step 4 > volume #1 style surface region 0,0,0,799,799,799 step 4 > volume #2 region 0,0,0,799,799,799 step 4 > volume #2 style surface region 0,0,0,799,799,799 step 4 > volume #1 showOutlineBox false > volume #2 showOutlineBox false > volume #2 level 0.02 > volume #2 change image level -0.0009087,0 level 0.02434,0.8 level 0.03987,1 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.01 > hide #!2 models > show #!1 models > volume #1 level 0.015 > volume #1 change image level -0.0008747,0 level 0.01593,0.8 level 0.02483,1 > volume #1 level 0.01 > hide #!1 models > show #!2 models > vop resample #2 onGrid #1 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > vop subtract #1 #3 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > volume #4 level 0.005 > shape icosahedron radius 450 divisions 1 color yellow > marker fromMesh #5 edgeRadius 6.0 color yellow > color radial #4 center 0,0,0 palette ^puor range 300,500 > volume #4 level 0.007 > volume #4 level 0.006 > color radial #4 center 0,0,0 palette ^rdgy range 300,500 > view initial > view orient > set bgColor white Fetching url http://www.colourlovers.com/api/palettes?keywords=BlGy&format=json&numResults=100 failed: HTTP Error 500: Internal Server Error > palette list No custom palettes. 315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > color radial #4 center 0,0,0 palette rdbu range 300,500 > color radial #4 center 0,0,0 palette ^rdbu range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-3 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-4 range 300,500 > select clear > color radial #4 center 0,0,0 palette ^rdbu-5 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-6 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-4 range 300,500 > ui tool show ""Side View"" > lighting soft > lighting full > lighting soft > hide #!5 models > show #5 models > lighting full > save ad5wt_ad5wtdeltaIX.tiff supersample 3 > lighting soft > lighting full > lighting soft > view name view1 > save /export0/people/vsreddy/data/Ad5_DeltaIX/ad5_deltaIX.cxs > lighting simple > view view1 > lighting full > volume #4 level 0.01 > view view1 > lighting full > lighting soft > lighting full > save ad5wt_ad5wtdeltaIX_highcont.tiff supersample 3 > save /export0/people/vsreddy/data/Ad5_DeltaIX/ad5_deltaIX.cxs ——— End of log from Sun Sep 17 10:41:16 2023 ——— opened ChimeraX session > lighting soft > lighting full > volume #4 level 0.02 > volume #4 level 0.01 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > view list Named views: view1 > view view1 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > hide #5.1 models > hide #5.2 models > hide #6 models > hide #!5 models > hide #!4 models > show #5 models > show #6 models > hide #6 models > hide #!5 models > show #!4 models > volume #4 style image region 0,0,399,799,799,399 step 1 originIndex > 399.5,399.5,399.5 showOutlineBox false > set bgColor black > volume #2 style image region 0,0,399,799,799,399 step 1 originIndex > 399.5,399.5,399.5 showOutlineBox false > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #4 red > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #4 #e01b24ff models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > open phenix_p9.pdb Chain information for phenix_p9.pdb #7 --- Chain | Description Q | No description available R | No description available S | No description available T | No description available > sym #7 I,222 Made 60 graphical clones for phenix_p9.pdb symmetry I,222 > ui tool show ""Side View"" > hide #!2 models > color #7 cyan > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > save diffmap_only_crossec.tiff supersample 3 > show #!7 models > save diffmap_p9model_crossec.tiff supersample 3 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > hide #!7 models > hide #!4 models > show #!4 models > view list Named views: view1 > view name view2 > view view2 > view view1 > color radial #4 center 0,0,0 palette ^puor range 300,500 > color radial #4 center 0,0,0 palette ^rdgy range 300,500 > color radial #4 center 0,0,0 palette rdgy range 300,500 > palette list No custom palettes. 315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > color radial #4 center 0,0,0 palette ylorrd range 300,500 > show #5 models > hide #5.1 models > show #6 models > set bgColor white > color radial #4 center 0,0,0 palette ylorrd-3 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-4 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-5 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-6 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-7 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-8 range 300,500 Fetching url http://www.colourlovers.com/api/palettes?keywords=YlOrRd-9&format=json&numResults=100 failed: HTTP Error 500: Internal Server Error > color radial #4 center 0,0,0 palette ylorrd-7 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-8 range 300,500 > color radial #4 center 0,0,0 palette ylorrd range 300,500 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.001 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > hide #!5 models > show #!7 models > hide #!7 models > hide #6 models > view view2 > color #4 red > set bgColor black > save diffmap_only_crossec_surf.tiff supersample 3 > show #!2 models > save diffmap_n_hexon_crossec_surf.tiff supersample 3 > hkcage 5 0 radius 450 color black > hide #!2 models > set bgColor white > view view1 > show #5 models > hide #5.1 models > color radial #4 center 0,0,0 palette ylorrd range 300,500 > show #6 models > show #5.1 models > hode #8 models Unknown command: hode #8 models > hide #8 models > show #8 models > open movie_diffmap_rock.cxc > view view1 > hide #8 models > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 120 > wait 120 > view view1 > wait 2 > show #8 models > rock y -30 120 > wait 120 > view view1 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y 30 120 > wait 120 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs ——— End of log from Thu Sep 21 18:27:05 2023 ——— opened ChimeraX session > hide #8 models > hide #6 models > hide #!5 models > hide #!4 models > show #!1 models > volume #1 level 0.007 > volume #1 level 0.006 > color radial #1 center 0,0,0 palette ^puor range 300,500 > volume #1 level 0.005 > volume #1 step 1 > volume #1 level 0.006 > volume #1 level 0.007 > open cmass_ad5_60_renum.pdb No such file/path: cmass_ad5_60_renum.pdb > open cmass_ad5_60_renum.pdb Chain information for cmass_ad5_60_renum.pdb #9 --- Chain | Description X | No description available > hide #!1 models > select #9 420 atoms, 419 pseudobonds, 420 residues, 2 models selected > style sel sphere Changed 420 atom styles > color (#!9 & sel) red > set #9 radius=2 Expected a keyword > setattr #9 radius=2 Missing or invalid ""attrName"" argument: Expected a text string > setattr #9 atom radius=2 Missing or invalid ""attrValue"" argument: Expected a text string > setattr #9 Atom radius=2 Missing or invalid ""attrValue"" argument: Expected a text string > setattr #9 atom radius 2 Assigning radius attribute to 420 items > setattr #9 atom radius 10 Assigning radius attribute to 420 items > show sel atoms > setattr #9 atom radius 10 color red Expected a keyword > select clear > setattr #9 atom radius=10 Missing or invalid ""attrValue"" argument: Expected a text string > close #9 > open tmp.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 50 Assigning radius attribute to 420 items > setattr #9 atom radius 20 Assigning radius attribute to 420 items > close #9 > open cmass_ad5_60.pdb Summary of feedback from opening cmass_ad5_60.pdb --- warnings | Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 54 messages similar to the above omitted > close #9 > open cmass60_tmp1.pdb > show #9 atoms > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > close #9 > open cmass60_tmp1.pdb > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > close #9 > open cmass60_tmp1.pdb > show #9 atoms > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > style #9 sphere Changed 420 atom styles > close #9 > open cmass60_tmp1.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 20 Assigning radius attribute to 420 items > setattr #9:HX1 color red Missing or invalid ""attrValue"" argument: Expected a text string > color #9:HX1 red > close #9 > open cmass_ad5_60_renum.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 20 Assigning radius attribute to 420 items > color #9:HX1 cornflowerblue > color #9:HX2 red > color #9:HX3 limegreen > color #9:HX4 gold > color #9:P3A forestgreen > color #9:HX3 lightbgreen Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #9:HX3 lightgreen > color #9:p8A yellow > color #9:p8B orange > color #9:HX4 khaki > show #!1 models > hide #!1 models > view view1 > ui tool show ""Side View"" > show #!1 models > hide #!1 models > show #!1 models > lighting soft > lighting simple > lighting soft > open movie_rock2.cxc > view view2 > movie record > rock y 30 180 > wait 180 > view view2 > wait 2 > hide #1 models > rock y -30 180 > wait 180 > view view2 > wait 2 > movie encode movie_ad5wt_markers.mp4 Movie saved to movie_ad5wt_markers.mp4 executed movie_rock2.cxc > view list Named views: view1, view2 > view view1 > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs ——— End of log from Thu Sep 21 21:26:56 2023 ——— opened ChimeraX session > show #1 models > lighting full > open movie_rock2.cxc > view view1 > hide #9 models > movie record > rock y 30 180 > wait 180 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Thu Sep 21 21:26:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Thu Sep 21 18:27:05 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ad5_deltaIX.cxs Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 4, values float32 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at level 0.01, step 1, values float32 Log from Sun Sep 17 10:41:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ad5wt_re3d_ctfref.mrc Opened ad5wt_re3d_ctfref.mrc as #1, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > open ad5wt_deltaIX_re3d_ctfref.mrc Opened ad5wt_deltaIX_re3d_ctfref.mrc as #2, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > ui tool show ""Map Coordinates"" > view orient > view initial > volume #1 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 style image region 0,0,396,799,799,396 step 1 showOutlineBox true > volume #1 style image region 0,0,396,799,799,396 step 1 showOutlineBox true > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > volume #1 region 0,0,0,799,799,799 step 4 > volume #1 style surface region 0,0,0,799,799,799 step 4 > volume #2 region 0,0,0,799,799,799 step 4 > volume #2 style surface region 0,0,0,799,799,799 step 4 > volume #1 showOutlineBox false > volume #2 showOutlineBox false > volume #2 level 0.02 > volume #2 change image level -0.0009087,0 level 0.02434,0.8 level 0.03987,1 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.01 > hide #!2 models > show #!1 models > volume #1 level 0.015 > volume #1 change image level -0.0008747,0 level 0.01593,0.8 level 0.02483,1 > volume #1 level 0.01 > hide #!1 models > show #!2 models > vop resample #2 onGrid #1 Opened ad5wt_deltaIX_re3d_ctfref.mrc resampled as #3, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > vop subtract #1 #3 Opened volume difference as #4, grid size 800,800,800, pixel 1.41, shown at step 1, values float32 > volume #4 level 0.005 > shape icosahedron radius 450 divisions 1 color yellow > marker fromMesh #5 edgeRadius 6.0 color yellow > color radial #4 center 0,0,0 palette ^puor range 300,500 > volume #4 level 0.007 > volume #4 level 0.006 > color radial #4 center 0,0,0 palette ^rdgy range 300,500 > view initial > view orient > set bgColor white Fetching url http://www.colourlovers.com/api/palettes?keywords=BlGy&format=json&numResults=100 failed: HTTP Error 500: Internal Server Error > palette list No custom palettes. 315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > color radial #4 center 0,0,0 palette rdbu range 300,500 > color radial #4 center 0,0,0 palette ^rdbu range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-3 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-4 range 300,500 > select clear > color radial #4 center 0,0,0 palette ^rdbu-5 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-6 range 300,500 > color radial #4 center 0,0,0 palette ^rdbu-4 range 300,500 > ui tool show ""Side View"" > lighting soft > lighting full > lighting soft > hide #!5 models > show #5 models > lighting full > save ad5wt_ad5wtdeltaIX.tiff supersample 3 > lighting soft > lighting full > lighting soft > view name view1 > save /export0/people/vsreddy/data/Ad5_DeltaIX/ad5_deltaIX.cxs > lighting simple > view view1 > lighting full > volume #4 level 0.01 > view view1 > lighting full > lighting soft > lighting full > save ad5wt_ad5wtdeltaIX_highcont.tiff supersample 3 > save /export0/people/vsreddy/data/Ad5_DeltaIX/ad5_deltaIX.cxs ——— End of log from Sun Sep 17 10:41:16 2023 ——— opened ChimeraX session > lighting soft > lighting full > volume #4 level 0.02 > volume #4 level 0.01 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > view list Named views: view1 > view view1 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > hide #5.1 models > hide #5.2 models > hide #6 models > hide #!5 models > hide #!4 models > show #5 models > show #6 models > hide #6 models > hide #!5 models > show #!4 models > volume #4 style image region 0,0,399,799,799,399 step 1 originIndex > 399.5,399.5,399.5 showOutlineBox false > set bgColor black > volume #2 style image region 0,0,399,799,799,399 step 1 originIndex > 399.5,399.5,399.5 showOutlineBox false > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #4 red > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #4 #e01b24ff models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > open phenix_p9.pdb Chain information for phenix_p9.pdb #7 --- Chain | Description Q | No description available R | No description available S | No description available T | No description available > sym #7 I,222 Made 60 graphical clones for phenix_p9.pdb symmetry I,222 > ui tool show ""Side View"" > hide #!2 models > color #7 cyan > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > save diffmap_only_crossec.tiff supersample 3 > show #!7 models > save diffmap_p9model_crossec.tiff supersample 3 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.008 > showOutlineBox false > hide #!7 models > hide #!4 models > show #!4 models > view list Named views: view1 > view name view2 > view view2 > view view1 > color radial #4 center 0,0,0 palette ^puor range 300,500 > color radial #4 center 0,0,0 palette ^rdgy range 300,500 > color radial #4 center 0,0,0 palette rdgy range 300,500 > palette list No custom palettes. 315 builtin palettes: Accent, Accent-3, Accent-4, Accent-5, Accent-6, Accent-7, Accent-8, alphafold, blue-white-red, bluered, Blues, Blues-3, Blues-4, Blues-5, Blues-6, Blues-7, Blues-8, Blues-9, BrBG, BrBG-10, BrBG-11, BrBG-3, BrBG-4, BrBG-5, BrBG-6, BrBG-7, BrBG-8, BrBG-9, BuGn, BuGn-3, BuGn-4, BuGn-5, BuGn-6, BuGn-7, BuGn-8, BuGn-9, BuPu, BuPu-3, BuPu-4, BuPu-5, BuPu-6, BuPu-7, BuPu-8, BuPu-9, cyan-gray-maroon, cyan-white-maroon, cyanmaroon, Dark2, Dark2-3, Dark2-4, Dark2-5, Dark2-6, Dark2-7, Dark2-8, esmfold, GnBu, GnBu-3, GnBu-4, GnBu-5, GnBu-6, GnBu-7, GnBu-8, GnBu-9, gray, grayscale, Greens, Greens-3, Greens-4, Greens-5, Greens-6, Greens-7, Greens-8, Greens-9, Greys, Greys-3, Greys-4, Greys-5, Greys-6, Greys-7, Greys-8, Greys-9, lipophilicity, Oranges, Oranges-3, Oranges-4, Oranges-5, Oranges-6, Oranges-7, Oranges-8, Oranges-9, OrRd, OrRd-3, OrRd-4, OrRd-5, OrRd-6, OrRd-7, OrRd-8, OrRd-9, pae, paecontacts, paegreen, Paired, Paired-10, Paired-11, Paired-12, Paired-3, Paired-4, Paired-5, Paired-6, Paired-7, Paired-8, Paired-9, Pastel1, Pastel1-3, Pastel1-4, Pastel1-5, Pastel1-6, Pastel1-7, Pastel1-8, Pastel1-9, Pastel2, Pastel2-3, Pastel2-4, Pastel2-5, Pastel2-6, Pastel2-7, Pastel2-8, PiYG, PiYG-10, PiYG-11, PiYG-3, PiYG-4, PiYG-5, PiYG-6, PiYG-7, PiYG-8, PiYG-9, PRGn, PRGn-10, PRGn-11, PRGn-3, PRGn-4, PRGn-5, PRGn-6, PRGn-7, PRGn-8, PRGn-9, PuBu, PuBu-3, PuBu-4, PuBu-5, PuBu-6, PuBu-7, PuBu-8, PuBu-9, PuBuGn, PuBuGn-3, PuBuGn-4, PuBuGn-5, PuBuGn-6, PuBuGn-7, PuBuGn-8, PuBuGn-9, PuOr, PuOr-10, PuOr-11, PuOr-3, PuOr-4, PuOr-5, PuOr-6, PuOr-7, PuOr-8, PuOr-9, PuRd, PuRd-3, PuRd-4, PuRd-5, PuRd-6, PuRd-7, PuRd-8, PuRd-9, Purples, Purples-3, Purples-4, Purples-5, Purples-6, Purples-7, Purples-8, Purples-9, rainbow, RdBu, RdBu-10, RdBu-11, RdBu-3, RdBu-4, RdBu-5, RdBu-6, RdBu-7, RdBu-8, RdBu-9, RdGy, RdGy-10, RdGy-11, RdGy-3, RdGy-4, RdGy-5, RdGy-6, RdGy-7, RdGy-8, RdGy-9, RdPu, RdPu-3, RdPu-4, RdPu-5, RdPu-6, RdPu-7, RdPu-8, RdPu-9, RdYlBu, RdYlBu-10, RdYlBu-11, RdYlBu-3, RdYlBu-4, RdYlBu-5, RdYlBu-6, RdYlBu-7, RdYlBu-8, RdYlBu-9, RdYlGn, RdYlGn-10, RdYlGn-11, RdYlGn-3, RdYlGn-4, RdYlGn-5, RdYlGn-6, RdYlGn-7, RdYlGn-8, RdYlGn-9, red-white-blue, redblue, Reds, Reds-3, Reds-4, Reds-5, Reds-6, Reds-7, Reds-8, Reds-9, Set1, Set1-3, Set1-4, Set1-5, Set1-6, Set1-7, Set1-8, Set1-9, Set2, Set2-3, Set2-4, Set2-5, Set2-6, Set2-7, Set2-8, Set3, Set3-10, Set3-11, Set3-12, Set3-3, Set3-4, Set3-5, Set3-6, Set3-7, Set3-8, Set3-9, Spectral, Spectral-10, Spectral-11, Spectral-3, Spectral-4, Spectral-5, Spectral-6, Spectral-7, Spectral-8, Spectral-9, YlGn, YlGn-3, YlGn-4, YlGn-5, YlGn-6, YlGn-7, YlGn-8, YlGn-9, YlGnBu, YlGnBu-3, YlGnBu-4, YlGnBu-5, YlGnBu-6, YlGnBu-7, YlGnBu-8, YlGnBu-9, YlOrBr, YlOrBr-3, YlOrBr-4, YlOrBr-5, YlOrBr-6, YlOrBr-7, YlOrBr-8, YlOrBr-9, YlOrRd, YlOrRd-3, YlOrRd-4, YlOrRd-5, YlOrRd-6, YlOrRd-7, and YlOrRd-8. > color radial #4 center 0,0,0 palette ylorrd range 300,500 > show #5 models > hide #5.1 models > show #6 models > set bgColor white > color radial #4 center 0,0,0 palette ylorrd-3 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-4 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-5 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-6 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-7 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-8 range 300,500 Fetching url http://www.colourlovers.com/api/palettes?keywords=YlOrRd-9&format=json&numResults=100 failed: HTTP Error 500: Internal Server Error > color radial #4 center 0,0,0 palette ylorrd-7 range 300,500 > color radial #4 center 0,0,0 palette ylorrd-8 range 300,500 > color radial #4 center 0,0,0 palette ylorrd range 300,500 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.001 > showOutlineBox false > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > open movie_diffmap_rock.cxc > view view1 > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 180 > wait 180 > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y -30 180 > wait 180 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > hide #!5 models > show #!7 models > hide #!7 models > hide #6 models > view view2 > color #4 red > set bgColor black > save diffmap_only_crossec_surf.tiff supersample 3 > show #!2 models > save diffmap_n_hexon_crossec_surf.tiff supersample 3 > hkcage 5 0 radius 450 color black > hide #!2 models > set bgColor white > view view1 > show #5 models > hide #5.1 models > color radial #4 center 0,0,0 palette ylorrd range 300,500 > show #6 models > show #5.1 models > hode #8 models Unknown command: hode #8 models > hide #8 models > show #8 models > open movie_diffmap_rock.cxc > view view1 > hide #8 models > movie record > view view1 > wait 2 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.007 > showOutlineBox false > rock y 30 120 > wait 120 > view view1 > wait 2 > show #8 models > rock y -30 120 > wait 120 > view view1 > volume #4 style surface region 0,0,0,799,799,799 step 1 level 0.01 > showOutlineBox false > rock y 30 120 > wait 120 > view view1 > wait 2 > movie encode movie_diffmap_3.9A.mp4 Movie saved to movie_diffmap_3.9A.mp4 executed movie_diffmap_rock.cxc > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs ——— End of log from Thu Sep 21 18:27:05 2023 ——— opened ChimeraX session > hide #8 models > hide #6 models > hide #!5 models > hide #!4 models > show #!1 models > volume #1 level 0.007 > volume #1 level 0.006 > color radial #1 center 0,0,0 palette ^puor range 300,500 > volume #1 level 0.005 > volume #1 step 1 > volume #1 level 0.006 > volume #1 level 0.007 > open cmass_ad5_60_renum.pdb No such file/path: cmass_ad5_60_renum.pdb > open cmass_ad5_60_renum.pdb Chain information for cmass_ad5_60_renum.pdb #9 --- Chain | Description X | No description available > hide #!1 models > select #9 420 atoms, 419 pseudobonds, 420 residues, 2 models selected > style sel sphere Changed 420 atom styles > color (#!9 & sel) red > set #9 radius=2 Expected a keyword > setattr #9 radius=2 Missing or invalid ""attrName"" argument: Expected a text string > setattr #9 atom radius=2 Missing or invalid ""attrValue"" argument: Expected a text string > setattr #9 Atom radius=2 Missing or invalid ""attrValue"" argument: Expected a text string > setattr #9 atom radius 2 Assigning radius attribute to 420 items > setattr #9 atom radius 10 Assigning radius attribute to 420 items > show sel atoms > setattr #9 atom radius 10 color red Expected a keyword > select clear > setattr #9 atom radius=10 Missing or invalid ""attrValue"" argument: Expected a text string > close #9 > open tmp.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 50 Assigning radius attribute to 420 items > setattr #9 atom radius 20 Assigning radius attribute to 420 items > close #9 > open cmass_ad5_60.pdb Summary of feedback from opening cmass_ad5_60.pdb --- warnings | Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 Duplicate atom serial number found: 87851 54 messages similar to the above omitted > close #9 > open cmass60_tmp1.pdb > show #9 atoms > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > close #9 > open cmass60_tmp1.pdb > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > close #9 > open cmass60_tmp1.pdb > show #9 atoms > setattr #9 atom radius 20 Assigning radius attribute to 420 items > show #9 atoms > style #9 sphere Changed 420 atom styles > close #9 > open cmass60_tmp1.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 20 Assigning radius attribute to 420 items > setattr #9:HX1 color red Missing or invalid ""attrValue"" argument: Expected a text string > color #9:HX1 red > close #9 > open cmass_ad5_60_renum.pdb > show #9 atoms > style #9 sphere Changed 420 atom styles > setattr #9 atom radius 20 Assigning radius attribute to 420 items > color #9:HX1 cornflowerblue > color #9:HX2 red > color #9:HX3 limegreen > color #9:HX4 gold > color #9:P3A forestgreen > color #9:HX3 lightbgreen Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #9:HX3 lightgreen > color #9:p8A yellow > color #9:p8B orange > color #9:HX4 khaki > show #!1 models > hide #!1 models > view view1 > ui tool show ""Side View"" > show #!1 models > hide #!1 models > show #!1 models > lighting soft > lighting simple > lighting soft > open movie_rock2.cxc > view view2 > movie record > rock y 30 180 > wait 180 > view view2 > wait 2 > hide #1 models > rock y -30 180 > wait 180 > view view2 > wait 2 > movie encode movie_ad5wt_markers.mp4 Movie saved to movie_ad5wt_markers.mp4 executed movie_rock2.cxc > view list Named views: view1, view2 > view view1 > save /export0/people/vsreddy/data/Ad5_WT/ad5_deltaIX.cxs ——— End of log from Thu Sep 21 21:26:56 2023 ——— opened ChimeraX session OpenGL version: 3.3.0 NVIDIA 535.104.05 OpenGL renderer: NVIDIA T400 4GB/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: Dell Inc. Model: Precision 5860 Tower OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 16 Intel(R) Xeon(R) w3-2435 Cache Size: 23040 KB Memory: total used free shared buff/cache available Mem: 125Gi 5.2Gi 115Gi 5.0Mi 4.6Gi 118Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 55:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 5000] [10de:1eb0] (rev a1) Subsystem: Dell TU104GL [Quadro RTX 5000] [1028:129f] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Input/Output nonchimerax all ChimeraX